The Twa were the original inhabitants of Burundi and were followed (c.AD 1000), and then outnumbered, by the Hutus. Probably in the 15th cent., the Tutsis migrated into the area, gained dominance over the Hutus, and established several states. By the 19th cent., the country was ruled by the mwami (king)—a Tutsi who controlled the other Tutsis of the region in a vassal relationship. In 1890, Burundi (along with Rwanda) became part of German East Africa, but the Germans began to govern the area only in 1897. During World War I, Belgian forces occupied (1916) Burundi, and in 1919 it became part of the Belgian League of Nations mandate of Ruanda-Urundi (which in 1946 became a UN trust territory). Under the German and Belgian administrations Christianity was spread, but the traditional social structure of Burundi was not altered, and there was little economic development.

On July 1, 1962, the country became an independent kingdom ruled by the mwami of Burundi. The mid-1960s were marked by fighting between the Tutsis and Hutus and by struggles for power among the Tutsis. In 1965 a coup attempted by Hutus failed, and the Tutsis retaliated by executing most Hutu political leaders and many other Hutus. In July, 1966, Mwambutsa IV was deposed by his son, who became Ntare V. The new ruler was himself deposed by a military coup in Nov., 1966, when a republic was established.

Michel Micombero, a Tutsi who had been appointed prime minister in 1966, became president; a new constitution was adopted in 1970. Renewed fighting between Tutsis and Hutus in the early 1970s resulted in the death of many thousands of Hutus. In 1972 a rebellion attempting to return Ntare V to power was crushed by the government; Ntare was executed and the Hutus were further repressed. In 1976, Micombero was overthrown by Col. Jean-Baptiste Bagaza (also a Tutsi), who became president and consolidated the Tutsi stranglehold on political power. His authoritarian rule led to conflict with the Roman Catholic Church, and many priests and missionaries suspected of sympathizing with the Hutu population were expelled in 1985.

Pierre Buyoya, a Tutsi and army major, became Burundi's head of state after a coup ousted Bagaza in 1987. Outcry after a Hutu uprising the following year was again brutally suppressed led to reforms designed to lessen ethnic divisions. Buyoya appointed a majority of Hutus to the cabinet, including the prime minister, and encouraged enlistment of Hutus in the military. Many Hutus had fled Burundi in 1988 and settled in Tanzania, but by mid-1989 most of them had returned.

A new constitution adopted in 1992 provided for a multiparty political system; in the 1993 elections, Melchior Ndadaye, a Hutu, defeated Buyoya to win the nation's first free presidential election. Soon afterward he was overthrown and killed in a coup attempt by Tutsi soldiers. Burundi was convulsed by ethnic violence in which thousands of Hutus and Tutsis died, and many fled the country. The coup collapsed, but civilian authority was restored slowly, and sporadic violence continued. In Apr., 1994, Cyprien Ntaryamira, a Hutu who had been chosen as president by parliament, was killed with the president of Rwanda when their plane crashed, possibly having been shot down. He was succeeded by Sylvestre Ntibantunganya, an ethnic Hutu, while a new power-sharing arrangement provided for a Tutsi prime minister.

Ntibantunganya, however, was unable to exercise control over the army. Fighting between Hutu militants, who had taken up arms after the 1993 coup and won control of much of NW Burundi, and Tutsi soldiers persisted, along with a high rate of civilian casualties and the continued flight of Hutus from the country. In July, 1996, the army overthrew the government, and Pierre Buyoya was once again installed as president. Uganda, Kenya, and Tanzania applied economic sanctions against the country in the wake of the coup but lifted them in 1999 as talks between the warring factions progressed. In Dec., 1999, Nelson Mandela was appointed by a group of African nations to act as a mediator in the conflict. An accord was reached in 2000, but some aspects of the agreement were left incomplete. In addition, two Hutu rebel groups refused to sign the accord, and young army officers unsuccessfully attempted to overthrow Buyoya twice in 2001.

In July, 2001, the Arusha accords, a Tutsi-Hutu power-sharing agreement, were finalized. Under them, Buyoya remained president, with a Hutu vice president (Domitien Ndayizeye), for 18 months; the new government was installed in Nov., 2001. Fighting with the Hutu rebel groups remained unaffected by both the accord and a Dec., 2002, cease-fire agreement with one of the rebel groups.

Ndayizeye succeeded Buyoya as transitional president in Apr., 2003, also for an 18-month term. Alphonse Kadege, a Tutsi, became vice president. At the same time, African Union observers began arriving in Burundi to monitor the peace. A peace accord with the National Council for the Defense of Democracy–Forces for the Defense of Democracy (CNDD-FDD), the main rebel group, was finalized in Nov., 2003, and CNDD-FDD representatives joined the government the next month. The smaller Forces for National Liberation (FNL) meanwhile continued attacks on the army. In Jan., 2004, the FNL participated in talks with the government for the first time, but no progress was made. In May, 2004, there were tensions between the CNDD-FDD and the main Tutsi and Hutu parties in the government, and the CNDD-FDD withdrew from the government for several months. The United Nations took over peacekeeping duties from the African Union the following month.

A constitution proposed in July was not signed by Tutsi parties, who wanted a guarantee that the presidency would alternate between Hutus and Tutsis and objected to the way seats were assigned in the legislature. Although a disproportionately large number of seats and government posts were guaranteed to Tutsi candidates, none of those seats were guaranteed to the candidates of Tutsi parties. The disagreement led to a cabinet boycott by the parties and stalled movement toward national elections, which were postponed until 2005. In Feb., 2005, however, the proposed constitution was overwhelmingly approved by Burundi's voters.

In Apr., 2005, the transitional period for the government was extended into Aug., 2005. The FNL agreed to a truce with government forces in May, but clashes continued to occur, and both sides were accused of violating the cease-fire. The CNDD-FDD won a majority of the seats in May's local council elections, a victory that prefigured its win in the June national assembly elections. Pierre Nkurunziza, leader of the CNDD-FDD, was elected president of Burundi in August.

The following month the FNL rejected holding peace talks with the new government. UN peacekeepers began withdrawing in Dec., 2005, and completed their withdrawal a year later. In May, 2006, the FNL and the government began talks, agreeing in principle in June to a cease-fire. A cease-fire was signed in September, and by June, 2007, some progess had been made in the negotiations. In July, however, the FNL broke off the talks; FNL dissidents split from the group, leading to FNL attacks on the dissidents in subsequent months. Clashes between the FNL and the government resumed as well.

Meanwhile, former president Ndayizeye and several others were arrested in Aug., 2006, on charges of plotting to assassinate Nkurunziza and overthrow the government (Ndayizeye and most of those arrested were acquitted in Jan., 2007), and in early September the vice president resigned, accusing the CNDD-FDD of corruption. The main opposition parties boycotted the parliament beginning in July, 2007, objecting to the composition of the cabinet; a new, more inclusive cabinet was formed in November.

In May, 2008, the FNL and the government again signed a cease-fire agreement, and in June the FNL leader announced an end to the Hutu rebel group's war against the government. In Dec., 2008, under pressure from foreign mediators, both sides committed to beginning the delayed implementation of their peace agreement, but the FNL did not disarm until Mar.–Apr., 2009. Despite the progress toward peace, political repression and politically motivated violence by both sides against individuals has continued.

The last of Burundi refugee camps in Uganda and Tanzania closed in 2009, and most refugees returned to Burundi, ending a process that had begun in 2002. However, many Burundian refugees who had fled to Tanzania in 1972 accepted an offer of Tanzanian citizenship. The CNDD-FDD won 64% in local elections in May, 2010; opposition parties accused the government of fraud, but foreign observers said the voting was generally free and fair, though the campaign had been marred by violence. The opposition candidates for president withdrew from the June presidential election, asserting it would be rigged, and Nkurunziza was reelected unopposed. The July legislative elections, which most opposition parties also boycotted, were won overwhelmingly by the CNDD-FDD.

The government subsequently moved to arrest a number of opposition leaders, some of whom fled Burundi, and engineered a replacement of the FNL leadership that aligned it with the ruling party. By the end of 2011, there was increasing evidence of politically related, often clandestine killings by government and opposition forces, and in Sept., 2012, the former leader of the FNL announced that the group had declared war on the CNDD-FDD government. In 2013, the government enacted a number of restrictions on press freedom. Politically related violence subsequently continued to be a problem.

The power-sharing government was threatened in 2014 after the president dismissed his Tutsi vice president and appointed another Tutsi to the post who lacked the support of UPRONA, the predominantly Tutsi party in the government. UPRONA ministers subsequently resigned from the cabinet, and the president replaced them with other UPRONA party members who lacked the party's support. In 2015 the president formalized plans to run for a third term, arguing that his first term was not an elected one, and secured the approval of the constitutional court, reportedly through intimidation. The move led to a series of antigovernment demonstrations that were suppressed by security forces and to an unsuccessful coup against the president; hundreds of thousands of Burundians, including the second vice president (who remained abroad until 2017), fled the country by the end of the year. Some former members of the Burundian military subsequently formed a rebel force in neighboring Congo (Kinshasa).

In the June, 2015, legislative elections the CNDD-FDD won most of the seats, and the president was reelected in July; both elections were boycotted by the opposition. Subsequently a number of prominent military and opposition figures were the target of assassinations and attempted assassinations, and violent attacks, by both government and opposition forces, increased. In Dec., 2015, the African Union announced it would send a 5,000-person peacekeeping force to Burundi, but Burundi's government rejected the force. In Oct., 2016, Burundi's government, which was the subject of a preliminary International Criminal Court investigation concerning political violence and torture, voted to withdraw from the ICC, and did so a year later. By the beginning of 2017, nearly 400,000 Burundians had fled the country, mainly to Tanzania, as a result of the continuing unrest. Also in 2016–17 the government increasingly purged and targeted Tutsi members of the armed forces. A new constitution approved in 2018 extended the presidential term to seven years, increased the president's powers, and made other changes, and also effectively allowed Nkurunziza to run for two more terms. In 2019 the more centrally located Gitega replaced Bujumbura as the country's capital. Nkurunziza ultimately decided not to run in 2020, and ruling party secretary general General Évariste Ndayishimiye won the presidency that May in a contest was marred by irregularties. The following month the president died and, though the constitution called for the president of the National Assembly to become interim president, the constitutional court ordered that the president-elect be sworn in.

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